title: ChIP-Seq analysis of H3K4me3 in human hES I3 TESR cells; 30DUMAAXX090620-5-S

description:
sample_term_id: NTR_0000836
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-12681
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2146
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2145
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM537626_BI.ES-I3.H3K4me3.Solexa-12681.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30DUMAAXX090620-5-S.hg19.level.1
ANALYSIS TITLE: Mapping of ES-I3 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the ES-I3 Cell Line, Library Solexa-12681 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4735
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.399
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.4174
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4534
POISSON_PERCENTILE: 47

**********************************************************************

ANALYSIS FILE NAME: GSM537626_BI.ES-I3.H3K4me3.Solexa-12681.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30DUMAAXX090620-5-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of ES-I3 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the ES-I3 Cell Line, Library Solexa-12681 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5009
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: ESI3 H3K4me3 81
BROWSER_TRACK_DESCRIPTION: BI ES-I3 Cell Line Histone H3K4me3 Library Solexa-12681 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.399
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.4174
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4534
POISSON_PERCENTILE: 47

**********************************************************************

source_name: I3(eye three) stem cells; 30DUMAAXX090620-5-S

value: TESR

value: SDS lysis

value: Bioruptor

value: 10 million cells


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in hESC H1 (hESC-01) Cells; renlab.H3K27me3.hESC-01.01

status: Public on Jan 07 2010

type: SRA

city: La Jolla

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

country: USA

institute: University of California, San Diego

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Library name: LL314
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1600
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1595

****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM466734_UCSD.H1.H3K27me3.UCSD_2008_09_25_5.bam
ANALYSIS ALIAS: UCSD.H3K27me3.Level1.2.4
ANALYSIS TITLE: Mapping of H1 H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K27me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1782
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

**********************************************************************

ANALYSIS FILE NAME: GSM466734_UCSD.H1.H3K27me3.UCSD_30RNPAAXX_4.bam
ANALYSIS ALIAS: UCSD.H3K27me3.Level1.2.1
ANALYSIS TITLE: Mapping of H1 H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K27me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1776
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

**********************************************************************

ANALYSIS FILE NAME: GSM466734_UCSD.H1.H3K27me3.UCSD_42B3BAAXX_7.bam
ANALYSIS ALIAS: UCSD.H3K27me3.Level1.2.2
ANALYSIS TITLE: Mapping of H1 H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K27me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1778
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

**********************************************************************

ANALYSIS FILE NAME: GSM466734_UCSD.H1.H3K27me3.UCSD_313BFAAXX_7.bam
ANALYSIS ALIAS: UCSD.H3K27me3.Level1.2.3
ANALYSIS TITLE: Mapping of H1 H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K27me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1780
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

**********************************************************************

ANALYSIS FILE NAME: GSM466734_UCSD.H1.H3K27me3.wig
ANALYSIS ALIAS: UCSD.H3K27me3.Level2.2.4
ANALYSIS TITLE: Raw Signal Density Graphs of H1 H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K27me3 in the H1 cell line were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1783
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

**********************************************************************

ANALYSIS FILE NAME: GSM466734_UCSD.H1.H3K27me3.LL314.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.hESC-01.01-renlab.H3K27me3.hESC-01.02-renlab.H3K27me3.hESC-01.03.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on the H1 Cell Line, Library LL314 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4401
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.4568
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.497
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9672
IROC_PERCENTILE: 81
POISSON_SCORE: 0.5322
POISSON_PERCENTILE: 77

**********************************************************************

ANALYSIS FILE NAME: GSM466734_UCSD.H1.H3K27me3.LL314.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.hESC-01.01-renlab.H3K27me3.hESC-01.02-renlab.H3K27me3.hESC-01.03.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the H1 Cell Line, Library LL314 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4494
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 H3K27me3 14
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K27me3 Library LL314 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.4568
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.497
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9672
IROC_PERCENTILE: 81
POISSON_SCORE: 0.5322
POISSON_PERCENTILE: 77

**********************************************************************

molecule: genomic DNA

organism: Homo sapiens

source_name: hESC-01; renlab.H3K27me3.hESC-01.01

extract_protocol:
Library construction protocol:
See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf

tag: molecule

value: genomic DNA

tag: disease

value: James Thompson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

tag: passage

value: Between 25 and 45

tag: medium

value: mTeSER

tag: Sex

value: Male

tag: batch

value: Histone H3K27me3

value: Branson Tip Sonicator

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Upstate


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in hESC H1 (hESC-01) Cells; renlab.H3K4me3.hESC-01.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Library name: LL312
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1636
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1595

****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM469971_UCSD.H1.H3K4me3.UCSD_2008_09_25_3.bam
ANALYSIS ALIAS: UCSD.H3K4me3.Level1.2.2
ANALYSIS TITLE: Mapping of H1 H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K4me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1768
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

**********************************************************************

ANALYSIS FILE NAME: GSM469971_UCSD.H1.H3K4me3.UCSD_312CNAAXX_4.bam
ANALYSIS ALIAS: UCSD.H3K4me3.Level1.2.1
ANALYSIS TITLE: Mapping of H1 H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K4me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1766
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

**********************************************************************

ANALYSIS FILE NAME: GSM469971_UCSD.H1.H3K4me3.wig
ANALYSIS ALIAS: UCSD.H3K4me3.Level2.2.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K4me3 in the H1 cell line were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1769
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

**********************************************************************

ANALYSIS FILE NAME: GSM469971_UCSD.H1.H3K4me3.LL312.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.hESC-01.01-renlab.H3K4me3.hESC-01.03.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the H1 Cell Line, Library LL312 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4420
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.7203
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.6914
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.741
POISSON_PERCENTILE: 94

**********************************************************************

ANALYSIS FILE NAME: GSM469971_UCSD.H1.H3K4me3.LL312.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.hESC-01.01-renlab.H3K4me3.hESC-01.03.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the H1 Cell Line, Library LL312 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4495
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 H3K4me3 12
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K4me3 Library LL312 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.7203
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.6914
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.741
POISSON_PERCENTILE: 94

**********************************************************************

source_name: hESC-01; renlab.H3K4me3.hESC-01.01

value: Histone H3K4me3

value: Abcam

value: unknown


title: ChIP-Seq analysis of WCE in mobilized CD34 cells; Lib:RI:20100517:01--ChIP:Thanh:20100504:01:Mobilized CD34:WCE

status: Public on Nov 12 2010

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

institute: Broad Institute

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20100517:01--ChIP:Thanh:20100504:01:Mobilized CD34:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3273
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3352
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM621689_BI.Mobilized_CD34_Primary_Cells.Input.UW_RO_01536.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100517:01--ChIP:Thanh:20100504:01:Mobilized CD34:WCE.hg19.level.1
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Mobilized CD34 Primary Cells, Donor RO 01536 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4579
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0065
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.0067
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.9794
IROC_PERCENTILE: 85
POISSON_SCORE: 0.2227
POISSON_PERCENTILE: 42

**********************************************************************

ANALYSIS FILE NAME: GSM621689_BI.Mobilized_CD34_Primary_Cells.Input.UW_RO_01536.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100517:01--ChIP:Thanh:20100504:01:Mobilized CD34:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Mobilized CD34 Primary Cells, Donor RO 01536 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4853
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MCD34 Input 36
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells ChIP-Seq Input Donor RO 01536 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0065
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.0067
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.9794
IROC_PERCENTILE: 85
POISSON_SCORE: 0.2227
POISSON_PERCENTILE: 42

**********************************************************************

source_name: CD34 cells mobilized into peripheral blood; Lib:RI:20100517:01--ChIP:Thanh:20100504:01:Mobilized CD34:WCE

extract_protocol: Library construction protocol: Single read - Illumina

tag: markers

value: Mobilized CD34

value: Hisp

value: Female

value: Primary Cell

value: UW

value: standard

value: SDS lysis

value: ChIP-Seq Input

value: Input

value: Bioruptor


title: ChIP-Seq analysis of H3K4me3 in Mobilized CD34 cells; Lib:RI:20100524:10--ChIP:MA:20100517:10:Mobilized CD34:H3K4Me3

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20100524:10--ChIP:MA:20100517:10:Mobilized CD34:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3779
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3881
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM621439_BI.Mobilized_CD34_Primary_Cells.H3K4me3.UW_RO_01549.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100524:10--ChIP:MA:20100517:10:Mobilized CD34:H3K4Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Mobilized CD34 Primary Cells, Donor RO 01549 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4657
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.6322
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.5962
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.9981
IROC_PERCENTILE: 37
POISSON_SCORE: 0.6523
POISSON_PERCENTILE: 81

**********************************************************************

ANALYSIS FILE NAME: GSM621439_BI.Mobilized_CD34_Primary_Cells.H3K4me3.UW_RO_01549.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100524:10--ChIP:MA:20100517:10:Mobilized CD34:H3K4Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01549 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4931
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MCD34 H3K4me3 49
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K4me3 Donor RO 01549 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.6322
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.5962
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.9981
IROC_PERCENTILE: 37
POISSON_SCORE: 0.6523
POISSON_PERCENTILE: 81

**********************************************************************

source_name: CD34 cells mobilized into peripheral blood; Lib:RI:20100524:10--ChIP:MA:20100517:10:Mobilized CD34:H3K4Me3

value: genomic DNA

value: Cauc

value: Protein A-Sepharose 4B

value: 10 million cells

value: 70 ul bed volume

value: Millipore


title: ChIP-Seq analysis of WCE in human H1 cells, 314G6AAXX090406-5-S

status: Public on Aug 05 2009

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Library name: Solexa-10531
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.1102
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.1103

****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM433179_BI.H1.input.FC_314G6AAXX_ln_5.bam
ANALYSIS TITLE: Mapping of H1 Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced as ChIP-Seq Input from the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1750
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

**********************************************************************

ANALYSIS FILE NAME: GSM433179_BI.H1.input.wig
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for Input in the H1 cell line were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1751
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

**********************************************************************

ANALYSIS FILE NAME: GSM433179_BI.H1.Input.Solexa-10531.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 314G6AAXX090406-5-S.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the H1 Cell Line, Library Solexa-10531 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4673
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0094
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.0894
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.3785
IROC_PERCENTILE: 27
POISSON_SCORE: 0.1752
POISSON_PERCENTILE: 13

**********************************************************************

ANALYSIS FILE NAME: GSM433179_BI.H1.Input.Solexa-10531.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 314G6AAXX090406-5-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the H1 Cell Line, Library Solexa-10531 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4947
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 Input 31
BROWSER_TRACK_DESCRIPTION: BI H1 Cell Line ChIP-Seq Input Library Solexa-10531 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0094
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.0894
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.3785
IROC_PERCENTILE: 27
POISSON_SCORE: 0.1752
POISSON_PERCENTILE: 13

**********************************************************************

value: Cellular Dynamics

value: Cell Line

value: undifferentiated

value: TESR

tag: sex

value: Unknown


title: NME-Pre TGF-2

status: Public on Jan 30 2014

type: RNA

city: West Lafayette

first: Michael

last: Wendt

state: IN

address: 201 S. University St.

department: MCMP

institute: Purdue University

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16hr at 45C on GeneChip Murine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The scanned dat files were converted to cel files using Affymetrix propriatary software Expression Console (EC). EC was also used to convert the cel files into spreadsheets of gene expression numbers using the RMA (Robust Multigene Analysis) feature of EC (RMA normalized data provided in sample table).  Raw data in logbase2 were converted into linear values and exported as a tab delimited text file along with appropriate annotations. Gene expression changes were defined as follows: The  group means were calculated for each gene.  Binary comparisons were generated  in which the group-mean ratio s were calculated for each gene. Raw data, group-means and group-mean ratios were imported into MS access data base manager. record were filtered for ratios >= 1.5 or <= 0.666666. Raw data (linear ) for each group were imported into BAMarray (Bayesian Analysis of Microarray data), a bootstrapping software  that uses z-values to confer statistical significance upon observed differences in the measurements.  Results for BAM analysis were imported into the same Access database and the BAM results cross-referenced to the group-mean ratios. Records that met both the group-mean ratio magnitude and BAM significance were deemed to be the differentially expressed genes (provided in the 'differentially_expressed.txt' series supplementary file)

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: NME-Pre TGF

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical manual, 2001, Affymetrix)

growth_protocol: DMEM containing 10% FBS and 10mg/ml Insulin

extract_protocol: Quaigen RNAeasy

treatment_protocol: 5 ng/ml TGF-beta1 for 4 weeks added every 4 days, then exogenous TGF-beta1 was withdrawn and cells were cultured for an additional 4 weeks.

tag: cell line background

value: NMumG

tag: cell type

value: normal murine mammary gland cells

tag: transformed by

value: overexpression of EGFR (NME)

tag: stimulated with

value: none (unstimuated control)


title: EpiHCMV vs Reference 6hpi

status: Public on Nov 10 2007

city: Princeton

first: Eain

middle: Anthony

last: Murphy

state: NJ

address: Lewis Thomas Laboratories

department: Molecular Biology

institute: Princeton University

description: EndoHCMV vs Reference 6hpi

hyb_protocol: reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=48835

scan_protocol: Pixel Size : 10 Scan Date : 2006-10-09 Scan Time : 14:59:57 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : A.7.5.1
Datafile type : Agilent result file
Lowess normalization & dye reversal

source_name: ARPE19s infected for 6h with EpiHCMV

growth_protocol: 6 hours post infection

extract_protocol: Trizol extraction

treatment_protocol: Infected at moi of 3

tag: endothelial generated HCMV

source_name: BD Universal reference RNA

extract_protocol: Commercial reference RNA

tag: Commercial reference RNA


title: FibroHCMV vs Reference 6hpi

description: FibroHCMV vs Reference 6hpi

source_name: ARPE19s infected for 6h with FibroHCMV

label_protocol: reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?i

tag: Fibroblast generated HCMV


title: EpiHCMV vs Reference 10hpi

description: EndoHCMV vs Reference 10hpi

source_name: ARPE19s infected for 10h with EpiHCMV

growth_protocol: 10 hours post infection


title: FibroHCMV vs Reference 10hpi

description: FibroHCMV vs Reference 10hpi

source_name: ARPE19s infected for 10h with FibroHCMV


title: Mock vs Reference

description: mock vs Reference

source_name: ARPE19s Mock infected

growth_protocol: mock infected

treatment_protocol: mock infected

tag: Mock infected fibroblasts